I don't think that WinCE has the "Manage GPS automatically" option Win Mob has that lets multiple apps share the GPS data.
Download this tool
ResInfoRun it and go to the tasks tab, That will show you what programmes are running, Clicking the processes box will tell you what hidden programmes are running, If you can do this when Navigon is running on it's own, AND when iGO is running you can tell if another process needs to be running to get GPS data, If both nav programmes are running together then kill Navigon and see if iGO picks up satellites, You may need to restart iGO.